Factions would be awsome. Just like those in Planescape Torment. For example we could join the Harpers they are most recognizable, there was even prestige class in NWN if I remember correctly. The rest of them as I've checked were Order of the Gauntlet, Emerald Enclave, Lords Alliance and Zhentarims.
Each individual faction could provide us with faction only quests through entire main campagin, some NPC's would react dependently of our choice, special rewards, faction alignment etc. What you guys think?